In the second episode, "Sentinel", the team encounters a computer containing vast amounts of data on advanced holographic technology - which later turns out to have been placed there by the Brassica. We also see some use of holography in "Light and Darkness", with Azrael, Vizznr and Cicissa who are intelligent, reactive holograms. This pays off later on, when the utter weirdness of the alien ship in "Though This Be Madness" can entirely be explained by the ship (or at least its interiors) being a hologram, including every single one of its passengers. This may also have been cleverly foreshadowed by Trelane's fictional town of Gothos, which is also entirely fictional (though its residents, in that case, are at least physically real).
If you get killed or captured during "Federation", you're treated to a cutscene showing Breddell's doomsday weapon firing at Earth and blowing it apart - with the U.S.S. Alexander blown clear from the explosion, causing it to travel back in time to meet the Enterprise again. This indicates that the Alexander was in Earth's orbit when the explosion occurred, and traveled back in time from that location. However, Kirk's Captain's Log recorded after the encounter indicates that they've "traced the Alexander's course back to Espoir Station", which makes no sense: The Alexander didn't come from Espoir Station; it came from Earth.